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From: NeuroMorpho A. <nm...@gm...> - 2023-12-05 17:41:37
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Dear colleagues, We're pleased to announce yesterday’s releases of NeuroMorpho.Org<https://neuromorpho.org/> Version 8.6 (12/4/23), with 14,452 new tracings from 45 datasets. The database currently tallies 260,078 digital reconstructions of neural morphology from 996 independent labs worldwide. Newly added functionalities include (i) a web-based universal converter<https://neuromorpho.org/xyz2swc/ui/> of morphological files from any existing format and tracing system into the SWC standard<https://www.nature.com/articles/s41467-023-42931-x>, and (ii) a bibliometric search<http://cng-nmo-dev3.orc.gmu.edu:8181/> allowing data contributors to monitor reusage<https://www.biorxiv.org/content/10.1101/2023.09.12.557386v1> of their shared datasets. Please visit the What's new<https://neuromorpho.org/WIN.jsp> and About<https://neuromorpho.org/about.jsp> pages for details on the growing content and features. We are continuously grateful to all data contributors<https://neuromorpho.org/acknowl.jsp> eager to share their hard-won morphologies with the research community. We apologize if you receive multiple versions of this message through cross-listing, and as always appreciate any and all feedback and comments. Sincerely, The NeuroMorpho.Org team<https://neuromorpho.org/acknowl.jsp#NMO> ---------------- Giorgio Ascoli<https://krasnow1.gmu.edu/cn3/ascoli>, PhD University Professor Bioengineering Department<https://bioengineering.gmu.edu/>, College of Engineering & Computing<https://cec.gmu.edu/> Neuroscience Program<https://neuroscience.gmu.edu/>, Krasnow Institute for Advanced Study<https://krasnow1.gmu.edu/> Director, Center for Neural Informatics, Structures, & Plasticity<https://krasnow1.gmu.edu/cn3> MS2A1 - George Mason University<https://www.gmu.edu/>, Fairfax, VA 22030-4444 Ph. +1(703)993-4383/+1(703)673-8894 Author of “Trees of the Brain, Roots of the Mind<https://www.amazon.com/Trees-Brain-Roots-Giorgio-Ascoli/dp/0262028980/>” (MIT Press, 2015<https://mitpress.mit.edu/9780262028981/trees-of-the-brain-roots-of-the-mind/>) Founding Editor-in-Chief, Neuroinformatics<https://link.springer.com/journal/12021> AIMBE<https://aimbe.org/> fellow |
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From: NeuroMorpho A. <nm...@gm...> - 2023-04-21 17:27:19
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Dear colleagues, We're pleased to announce yesterday’s releases of NeuroMorpho.Org<https://neuromorpho.org/index.jsp> Version 8.5 (4/20/23), with 13,597 new tracings from 67 datasets. The database currently tallies 245,626 digital reconstructions of neural morphology from 962 independent labs worldwide. Please visit the What's new<https://neuromorpho.org/WIN.jsp> and About<https://neuromorpho.org/about.jsp> pages for details on the growing content and features, or check out recent updates to literature coverage<https://neuromorpho.org/LS.jsp> and detailed usage statistics<https://neuromorpho.org/statistics.jsp>. We are continuously grateful to all data contributors<https://neuromorpho.org/acknowl.jsp#DC> eager to share their hard-won morphologies with the research community. We apologize if you receive multiple versions of this message through cross-listing, and as always appreciate any and all feedback and comments. Sincerely, The NeuroMorpho.Org team<https://neuromorpho.org/acknowl.jsp#NMO> ---------------- Giorgio Ascoli<https://krasnow1.gmu.edu/cn3/ascoli>, PhD University Professor Bioengineering Department<https://bioengineering.gmu.edu/>, College of Engineering & Computing<https://cec.gmu.edu/> Neuroscience Program<https://neuroscience.gmu.edu/>, Krasnow Institute for Advanced Study<https://krasnow1.gmu.edu/> Director, Center for Neural Informatics, Structures, & Plasticity<https://krasnow1.gmu.edu/cn3> MS2A1 - George Mason University<https://gmu.edu/>, Fairfax, VA 22030-4444 Ph. +1(703)993-4383/+1(703)673-8894 Author of “Trees of the Brain, Roots of the Mind<https://www.amazon.com/Trees-Brain-Roots-Giorgio-Ascoli/dp/0262028980/>” (MIT Press, 2015<https://mitpress.mit.edu/books/trees-brain-roots-mind>) Founding Editor-in-Chief, Neuroinformatics<https://link.springer.com/journal/12021> AIMBE<https://aimbe.org/> fellow |
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From: NeuroMorpho A. <nm...@gm...> - 2022-10-18 17:19:16
|
Dear colleagues, We're pleased to announce two new releases of NeuroMorpho.Org<https://neuromorpho.org/>. Version 8.4 (10/17/22) consisted of the largest individual-dataset release to date, with nearly 42,000 tracings from a single publication by the Siegert lab. Versions 8.3 (10/14/22) added over 16,000 tracings from 67 new datasets and introduced the new functionality of Semi-Automated Metadata Annotation<http://cng-nmo-meta.orc.gmu.edu/help/>. The database currently tallies 232,029 digital reconstructions of neural morphology, with glia now constituting almost one-third of the content. Please visit the What's new<https://neuromorpho.org/WIN.jsp> and About<https://neuromorpho.org/about.jsp> pages for details on the growing content and features, check out recent updates to literature coverage<https://neuromorpho.org/LS.jsp> and detailed usage statistics<https://neuromorpho.org/statistics.jsp>, or peruse our newest 90-second video<https://vimeo.com/752137686>. We are continuously grateful to all data contributors<https://neuromorpho.org/acknowl.jsp> from 922 labs worldwide eager to share their hard-won morphologies with the research community. We apologize if you receive multiple versions of this message through cross-listing, and as always appreciate any and all feedback and comments. Sincerely, The NeuroMorpho.Org team<https://neuromorpho.org/acknowl.jsp#NMO> ---------------- Giorgio Ascoli<http://krasnow1.gmu.edu/cn3/ascoli>, PhD University Professor Bioengineering Department<http://bioengineering.gmu.edu/>, Volgenau School of Engineering<http://volgenau.gmu.edu/> Neuroscience Program<http://neuroscience.gmu.edu/>, Krasnow Institute for Advanced Study<http://krasnow1.gmu.edu/> Director, Center for Neural Informatics, Structures, & Plasticity<http://krasnow1.gmu.edu/cn3> MS2A1 - George Mason University<http://gmu.edu/>, Fairfax, VA 22030-4444 Ph. +1(703)993-4383/+1(703)673-8894 Author of “Trees of the Brain, Roots of the Mind<http://www.amazon.com/Trees-Brain-Roots-Giorgio-Ascoli/dp/0262028980/>” (MIT Press, 2015<http://mitpress.mit.edu/books/trees-brain-roots-mind>) Founding Editor-in-Chief, Neuroinformatics<http://link.springer.com/journal/12021> AIMBE<https://aimbe.org/> fellow |
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From: John M. <so...@ho...> - 2020-10-09 19:22:43
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Hi, I am not able to code in any computer language. This is the proposed design script for the Film, working title, 'Converse Creation'. Its subject matter is response t I reuire o stimulus and stimuli over a linear time-period. I require software to generate dendrites (without having any raw data) other than utilising a quasi-input (User-Interface?) to determine dendrites' unique volume, size, growth and colour of the dendrite tree--where possible I would like to control all these features concerning the production of dendrites along the timeline. Dendrites' colours is a significant aspect with respect to flux and for the audience to perceive these generated dendrite(s) responses to a particular stimulus. I would like for each sequence of each new unique dendrite with its own unique growth/size/shape and colour to also be able to coalesce together. I would like for each unique coloured dendrite to superimpose and entangle together, and for all dendrites to uniformly adopt the same colour (become saturated with bursting), and then for each dendrite to fade back into each of its original discreet colours as their size shrinks or/and to hold onto the bursting colour. Can your software or does your software have a GUI to support these features with quasi inputs to define these features--volume, size, growth and colour--along a timeline? Kind Regards John Morrissey |
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From: NeuroMorpho A. <nm...@gm...> - 2020-06-30 22:47:03
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Dear colleagues, We're pleased to announce the June 29, 2020 release of NeuroMorpho.Org<http://neuromorpho.org/> Version 8.0, adding over 10,000 tracings from 65 new datasets and 11 new species. This major update brings the database total to 131,960 digital reconstructions of neuronal and glial morphology and streamlines the data publication process: forthcoming archives can be directly uploaded online<http://cng-nmo-meta.orc.gmu.edu/> and will be released as soon as their data and metadata have been processed. Please visit the What's new page<http://neuromorpho.org/WIN.jsp> for details on the growing content and functionality, and check out recent updates to the literature coverage<http://neuromorpho.org/LS.jsp> and detailed usage statistics<http://neuromorpho.org/statistics.jsp>. We are continuously grateful to all data contributors<http://neuromorpho.org/acknowl.jsp#DC> from 696 labs worldwide eager to share their hard-won tracings with the community. We apologize if you receive multiple versions of this message through cross-listing, and as always appreciate any and all feedback and comments. Sincerely, The NeuroMorpho.Org team<http://neuromorpho.org/acknowl.jsp#NMO> ---------------- Giorgio Ascoli<http://krasnow1.gmu.edu/cn3/ascoli>, PhD University Professor Bioengineering Department<http://bioengineering.gmu.edu/>, Volgenau School of Engineering<http://volgenau.gmu.edu/> Neuroscience Program<http://neuroscience.gmu.edu/>, Krasnow Institute for Advanced Study<http://krasnow1.gmu.edu/> Director, Center for Neural Informatics, Structures, & Plasticity<http://krasnow1.gmu.edu/cn3> MS2A1 - George Mason University<http://gmu.edu/>, Fairfax, VA 22030-4444 Ph. +1(703)993-4383/+1(703)673-8894 Author of “Trees of the Brain, Roots of the Mind<http://www.amazon.com/Trees-Brain-Roots-Giorgio-Ascoli/dp/0262028980/>” (MIT Press, 2015<http://mitpress.mit.edu/books/trees-brain-roots-mind>) Founding Editor-in-Chief, Neuroinformatics<http://link.springer.com/journal/12021> |
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From: NeuroMorpho A. <nm...@gm...> - 2020-04-02 00:18:39
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Dear Colleagues, You may have heard of Mozak, a citizen science project that presents raw image stacks of neuronal morphology from optical microscopy to players through a videogame platform enabling them to digitally reconstruct the corresponding dendritic and axonal trees in 3D (Roskam & Popovic, Neuron’16, doi.org/10.1016/j.neuron.2016.10.045). With many researchers housebound all around the globe during these challenging times, we are launching a friendly competition. We’re inviting teams from different labs and neuroscience departments anywhere in the world to enter www.mozak.science during an upcoming week and play against other labs (and against many citizen scientists!). Will you, your peers, trainees, colleagues, and students rise to the challenge and participate in this international neural tracing effort? It’s a unique opportunity to purposefully connect, joyfully focus on neurons, and advance science! We might start as early as next week (April 6-10) if feasible or the following week (April 13-17) otherwise. If you are interested in forming a team, just email me your timing preference, if any, at as...@gm.... Please let me know if you have any questions. Best, ---------------- Giorgio Ascoli, PhD University Professor Bioengineering Department, Volgenau School of Engineering Neuroscience Program, Krasnow Institute for Advanced Study Director, Center for Neural Informatics, Structures, & Plasticity MS2A1 - George Mason University, Fairfax, VA 22030-4444 (USA) Ph. +1(703)993-4383/+1(703)673-8894 Author of “Trees of the Brain, Roots of the Mind” (MIT Press, 2015) Founding Editor-in-Chief, Neuroinformatics |
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From: NeuroMorpho A. <nm...@gm...> - 2019-12-17 02:10:39
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Dear colleagues, We're pleased to announce the December 13, 2019 release of Version 7.9 of NeuroMorpho.Org<http://neuromorpho.org/>, adding nearly 10,000 tracings from 71 new datasets and bringing the database total to 121,544 digital reconstructions of neuronal and glial morphology. Please visit the What's new page<http://neuromorpho.org/WIN.jsp> for details on the growing data, metadata, and functionality, and check out recent updates to the literature coverage<http://neuromorpho.org/LS.jsp> and detailed usage statistics<http://neuromorpho.org/statistics.jsp> . We are continuously grateful to all data contributors<http://neuromorpho.org/acknowl.jsp#DC> from 647 labs worldwide eager to share their hard-won tracings with the community. We apologize if you receive multiple versions of this message through cross-listing, and as always appreciate any and all feedback and comments. Sincerely, The NeuroMorpho.Org team<http://neuromorpho.org/acknowl.jsp#NMO> ---------------- Giorgio Ascoli<http://krasnow1.gmu.edu/cn3/ascoli>, PhD University Professor Bioengineering Department<http://bioengineering.gmu.edu/>, Volgenau School of Engineering<http://volgenau.gmu.edu/> Neuroscience Program<http://neuroscience.gmu.edu/>, Krasnow Institute for Advanced Study<http://krasnow1.gmu.edu/> Director, Center for Neural Informatics, Structures, & Plasticity<http://krasnow1.gmu.edu/cn3> MS2A1 - George Mason University<http://gmu.edu/>, Fairfax, VA 22030-4444 Ph. +1(703)993-4383/+1(703)673-8894 Author of “Trees of the Brain, Roots of the Mind<http://www.amazon.com/Trees-Brain-Roots-Giorgio-Ascoli/dp/0262028980/>” (MIT Press, 2015<http://mitpress.mit.edu/books/trees-brain-roots-mind>) Founding Editor-in-Chief, Neuroinformatics<http://link.springer.com/journal/12021> |
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From: NeuroMorpho A. <nm...@gm...> - 2019-08-20 21:09:02
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Dear colleagues, We're pleased to announce the August 19, 2019 release of Version 7.8 of NeuroMorpho.Org<http://neuromorpho.org/>, adding 64 new datasets and bringing the database total to 112,244 digital reconstructions of neuronal and glial morphology. Please visit the What's new page<http://neuromorpho.org/WIN.jsp> for details on the evolving data, metadata, and functionality. The literature coverage<http://neuromorpho.org/LS.jsp> and detailed usage statistics<http://neuromorpho.org/statistics.jsp> were also updated, with more than 1700 articles employing, citing, or describing data in the repository, and nearly 20 million reconstructions downloaded. We are continuously grateful to all data contributors<http://neuromorpho.org/acknowl.jsp#DC> eager to share their hard-won tracings with the community. We apologize if you receive multiple versions of this message through cross-listing, and as always appreciate any and all feedback and comments. Sincerely, The NeuroMorpho.Org team<http://neuromorpho.org/acknowl.jsp#NMO> ---------------- Giorgio Ascoli<http://krasnow1.gmu.edu/cn3/ascoli>, PhD University Professor Bioengineering Department<http://bioengineering.gmu.edu/>, Volgenau School of Engineering<http://volgenau.gmu.edu/> Neuroscience Program<http://neuroscience.gmu.edu/>, Krasnow Institute for Advanced Study<http://krasnow1.gmu.edu/> Director, Center for Neural Informatics, Structures, & Plasticity<http://krasnow1.gmu.edu/cn3> MS2A1 - George Mason University<http://gmu.edu/>, Fairfax, VA 22030-4444 Ph. +1(703)993-4383/+1(703)673-8894 Author of “Trees of the Brain, Roots of the Mind<http://www.amazon.com/Trees-Brain-Roots-Giorgio-Ascoli/dp/0262028980/>” (MIT Press, 2015<http://mitpress.mit.edu/books/trees-brain-roots-mind>) Founding Editor-in-Chief, Neuroinformatics<http://link.springer.com/journal/12021> |
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From: Dave B. <db...@Co...> - 2019-06-10 21:02:53
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I would like to announce the Official Release of PGENESIS 2.4 along with a significant update to GENESIS 2.4. GENESIS is implemented with an object-oriented design that groups related object and command definitions into separately compiled libraries. Parallel GENESIS (PGENESIS) adds a library with a "postmaster" object to the usual usual GENESIS objects and commands. This allows a GENESIS simulation (e. g. a large network model) to be split into many MPI processes that communicate through the postmaster. The November 2014 release of GENESIS 2.4 was intended to be the last packaged GENESIS 2 distribution for download from the GENESIS web site (http://genesis-sim.org/GENESIS). As GENESIS is user-supported, rather than centrally developed, updates to GENESIS and PGENESIS are now obtained from the Repository for Continued Development of the GENESIS 2.4 Neural Simulator (https://github.com/genesis-sim/genesis-2.4). The object-oriented design and organization not only fosters the community development of neural models, but of the simulator itself. This new mutually-developed release of PGENESIS is such an example. As users have continued to contribute new libraries and improvements, there has been an increased use and extension of GENESIS and PGENESIS for its original purpose of realistically modeling cortical networks of multicompartmental neurons on parallel computers. Recent updates to GENESIS and a merge of the GENESIS/PGENESIS development branch from the U.S. Army Research Laboratory have addressed a number of issues in order to increase its scalability for modeling very large networks on high performance computing resources, allowing for models of millions of neurons. These improvements have made it necessary for a new release of a combined package of the May 2019 GENESIS 2.4 Update and the PGENESIS 2.4 Official Release. Information about this release and downloads are available from the GENESIS web site (http://genesis-sim.org/GENESIS). The official release of PGENESIS 2.4 is much improved from the December 2014 preliminary release. Updates of GENESIS since the 2014 release allow the fast "hsolve" solver to be used with new synaptic plasticity models and measurements of cortical field potentials. The efficient delivery of spike events when hsolve is used with large network models results in increases in simulation speed by factors of 10 to 20. This release of PGENESIS 2.4 is also now available for running large-scale network simulations on supercomputers at the Neuroscience Gateway Portal (NSG). For further information, see the https://www.nsgportal.org web page. Dave Beeman |
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From: NeuroMorpho A. <nm...@gm...> - 2018-10-07 10:20:15
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Dear Colleagues, We are searching for an exceptional individual to lead the information technology infrastructure of NeuroMorpho.Org as a Research Assistant Professor in the Center for Neural Informatics and the Bioengineering Department of George Mason University (near Washington DC, USA). If you know suitable candidates with a Ph.D. in computer science, software engineering, information systems, applied mathematics, physics, data science, or related fields, please encourage them to apply at jobs.gmu.edu/postings/44093 Especially desired are proficiency in Java, C/C++, Python, R, Matlab, and Shell scripting; experience with Unix/Linux server administration; SQL & NoSQL database design and system operation; web technologies and API (micro) services; content management & collaborative platforms; big-data & cloud computing analytical tools; task analysis automation; knowledge in project management (PMP or similar); and understanding of neuroscience data. The successful applicant will assume responsibility of the NeuroMorpho.Org continuous maintenance, development, and management, including design of new solutions to enhance and expand existing functionality. The incumbent will work directly with the project director, will select and supervise multiple masters-level assistants, and will have unlimited access to dedicated supercomputer and server facilities, flexible working schedule, salary based on the NIH scale, and state employee benefits. Review of applications will begin on November 1, 2018; the position is available immediately. Thank you in advance for helping NeuroMorpho.Org fill this crucial post. Best regards, The NeuroMorpho.Org Team ---------------- Giorgio Ascoli, PhD University Professor Bioengineering Department, Volgenau School of Engineering Neuroscience Program, Krasnow Institute for Advanced Study Director, Center for Neural Informatics, Structures, & Plasticity MS2A1 - George Mason University, Fairfax, VA 22030-4444 Ph. +1(703)993-4383/+1(703)673-8894 Author of "Trees of the Brain, Roots of the Mind" (MIT Press, 2015) Founding Editor-in-Chief, Neuroinformatics |
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From: Hugo C. <hug...@gm...> - 2018-09-22 09:40:41
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Hi Svetlana, To add randomization to the maximal conductance of a tabchannel, you can use the setrandfield command after the .p file has been read. This command can be used to randomize other fields to, or to randomize fields at each simulation step. Copying from the Genesis reference manual, at http://genesis-sim.org/GENESIS /Hyperdoc/Manual-25.html#ss25.146 25.154 setrandfield Routine Name: setrandfield Description: Sets an element field to a random value Usage: | [-uniform low high] setrandfield path field | [-gaussian mean sd] | [-exponential mid max] Example: setrandfield /pyr/pyramidal[]/HH_Na_channel \ X_alpha_V0 -gaussian -40 3 Notes: In the example above (from Scripts/piriform/pyramidal.g), setrandfield is being used to give some variation to the voltage dependence of the activation of Na channels used in all of the pyramidal cells used in the model. In this case, there is a gaussian distribution about the mean of -40 mV, with a standard deviation of 3 mV. Another use of the setrandfield comamnd would be to use it in script function to be executed as the command of a script_out object, or as the PROCESS action of an extended object, in order to randomly change a field at every time step. This would be a way to inject a noise current into a compartment, for example. The -uniform option gives a a random number taken from a uniform distribution in the range "low" to "high". The -exponential option gives a random number taken from an exponential distribution with a minimum value of zero, a 1/e point of "mid" and a maximum value of "max". Versions of GENESIS prior to 2.2 used a different interpretation of the two arguments. See also: setfield <http://genesis-sim.org/GENESIS/Hyperdoc/Manual-25.html#setfield> I hope this helps. Hugo On Fri, Sep 21, 2018 at 2:23 PM, Gladycheva, Svetlana < sgl...@to...> wrote: > Hello colleagues - > > > any wisdom of how to add randomization to tabchannel maximum conductance? > > cell.p file where max conductance parameter is read from, for example: > > > soma none 0 0 15 16 KA1 300 > > doesn't seem to allow to replace the number (300) with an expression > ({rand 200 400} ) or with a variable.. > > Thanks... > Svetlana > > > > > _______________________________________________ > Genesis-sim-users mailing list > Gen...@li... > https://lists.sourceforge.net/lists/listinfo/genesis-sim-users > > -- Hugo -- Hugo Cornelis, Ph.D. Agora Classica -- CTO http://www.agoraclassica.com/ GENESIS-3 -- lead architect http://www.genesis-sim.org/ |
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From: Gladycheva, S. <sgl...@to...> - 2018-09-21 12:58:10
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Hello colleagues -
any wisdom of how to add randomization to tabchannel maximum conductance?
cell.p file where max conductance parameter is read from, for example:
soma none 0 0 15 16 KA1 300
doesn't seem to allow to replace the number (300) with an expression ({rand 200 400} ) or with a variable..
Thanks...
Svetlana
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From: NeuroMorpho A. <nm...@gm...> - 2018-08-06 18:17:59
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Dear colleagues, We’re pleased to announce the August 2, 2018 release of Version 7.5 of NeuroMorpho.Org<http://neuromorpho.org/>, adding 9939 reconstructions from 31 new datasets. The repository now provides access to 96,831 cells from 823 peer-reviewed publications. A new data descriptor was added in the detailed neuron information page based on persistence diagrams. Please visit the What’s new page<http://neuromorpho.org/WIN.jsp> for details on the added data, metadata, and functionality. The literature coverage was also updated to include publications through July 2018. We are continuously grateful to all data contributors<http://neuromorpho.org/acknowl.jsp#DC> who freely share their hard-won tracings with the community. We appreciate any and all feedback and comments. Our apologies if you receive multiple versions of this message through cross-listing. Sincerely, The NeuroMorpho.Org team<http://neuromorpho.org/acknowl.jsp#NMO> ---------------- Giorgio Ascoli<http://krasnow1.gmu.edu/cn3/ascoli>, PhD University Professor Bioengineering Department<http://bioengineering.gmu.edu/>, Volgenau School of Engineering<http://volgenau.gmu.edu/> Neuroscience Program<http://neuroscience.gmu.edu/>, Krasnow Institute for Advanced Study<http://krasnow1.gmu.edu/> Director, Center for Neural Informatics, Structures, & Plasticity<http://krasnow1.gmu.edu/cn3> MS2A1 - George Mason University<http://gmu.edu/>, Fairfax, VA 22030-4444 Ph. +1(703)993-4383/+1(703)673-8894 Author of “Trees of the Brain, Roots of the Mind<http://www.amazon.com/Trees-Brain-Roots-Giorgio-Ascoli/dp/0262028980/>” (MIT Press, 2015<http://mitpress.mit.edu/books/trees-brain-roots-mind>) Founding Editor-in-Chief, Neuroinformatics<http://link.springer.com/journal/12021> |
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From: Furkan K. <fur...@at...> - 2018-07-23 11:01:58
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Dear All, As a part of Master's thesis research, I am conducting an online survey on software engineering practices and problems in developing cognitive and neuroscientific architectures/frameworks/simulators and computational models on those platforms. If you have been involved in developing such cognitive/neuroscientific modelling tools and computational models on them, we will be grateful if you could answer our survey questions in the link given below: http://moodle.atilim.edu.tr/anket/index.php?r=survey/index&sid=579941&lang=en [1] The participation is voluntary and anonymous; the survey will take about 10 minutes. We hope to better understand and develop suggestions for improving cognitive modelling and computational neuroscience software from a software engineering point of view at the end of our research. As a symbol of gratitude of your participation, participants who complete the survey will be eligible for a prize draw for a $40 book check from Amazon. Best Regards, -- Furkan Kurtaran Computer Engineering Department Research Assistant Atilim University https://www.atilim.edu.tr/en/compe/page/1595/academic-staff Links: ------ [1] http://moodle.atilim.edu.tr/anket/index.php?r=survey/index&sid=579941&lang=en |
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From: NeuroMorpho A. <nm...@gm...> - 2018-04-22 17:47:45
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Dear colleagues, We’re pleased to announce the April 16, 2018 release of Version 7.4 of NeuroMorpho.Org<http://neuromorpho.org/>, adding 6881 reconstructions from 57 new datasets. The repository now provides access to 86,893 cells from over 50 distinct animal species including numerous new entries (African wild dog, Aplysia, Banded mongoose, Blue wildebeest, Caracal, Clam worm, Ferret, Greater kudu, Lion, Mountain zebra, Red-necked wallaby, and Ring-tailed lemur). Please visit the What’s new page<http://neuromorpho.org/WIN.jsp> for details on the added data and metadata. The literature coverage was also updated to include publications through March 2018, with more than 30,000 mined articles. We are continuously grateful to all data contributors<http://neuromorpho.org/acknowl.jsp#DC> who freely share their hard-won tracings with the community. We appreciate any and all feedback and comments. Our apologies if you receive multiple versions of this message through cross-listing. Sincerely, The NeuroMorpho.Org team<http://neuromorpho.org/acknowl.jsp#NMO> ---------------- Giorgio Ascoli<http://krasnow1.gmu.edu/cn3/ascoli>, PhD University Professor Bioengineering Department<http://bioengineering.gmu.edu/>, Volgenau School of Engineering<http://volgenau.gmu.edu/> Neuroscience Program<http://neuroscience.gmu.edu/>, Krasnow Institute for Advanced Study<http://krasnow1.gmu.edu/> Director, Center for Neural Informatics, Structures, & Plasticity<http://krasnow1.gmu.edu/cn3> MS2A1 - George Mason University<http://gmu.edu/>, Fairfax, VA 22030-4444 Ph. +1(703)993-4383/+1(703)673-8894 Author of “Trees of the Brain, Roots of the Mind<http://www.amazon.com/Trees-Brain-Roots-Giorgio-Ascoli/dp/0262028980/>” (MIT Press, 2015<http://mitpress.mit.edu/books/trees-brain-roots-mind>) Founding Editor-in-Chief, Neuroinformatics<http://link.springer.com/journal/12021> |
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From: NeuroMorpho A. <nm...@gm...> - 2017-12-02 20:15:31
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Dear colleagues, We’re pleased to announce the November 28, 2017 release of Version 7.3 of NeuroMorpho.Org<http://neuromorpho.org/>, adding 9987 reconstructions from 96 new datasets. The repository now provides access to 80,012 cells and passed 8 million downloads in 166 countries. Please visit the What’s new page<http://neuromorpho.org/WIN.jsp> for details on the added data and metadata. The literature coverage was also updated to include publications through October 2017, with more than 1000 articles referencing data in this resource. We are continuously grateful to all data contributors<http://neuromorpho.org/acknowl.jsp#DC> who freely share their hard-won tracings with the community. We appreciate any and all feedback and comments. Our apologies if you receive multiple versions of this message through cross-listing. Sincerely, The NeuroMorpho.Org team<http://neuromorpho.org/acknowl.jsp#NMO> ---------------- Giorgio Ascoli<http://krasnow1.gmu.edu/cn3/ascoli>, PhD University Professor Bioengineering Department<http://bioengineering.gmu.edu/>, Volgenau School of Engineering<http://volgenau.gmu.edu/> Neuroscience Program<http://neuroscience.gmu.edu/>, Krasnow Institute for Advanced Study<http://krasnow1.gmu.edu/> Director, Center for Neural Informatics, Structures, & Plasticity<http://krasnow1.gmu.edu/cn3> MS2A1 - George Mason University<http://gmu.edu/>, Fairfax, VA 22030-4444 Ph. +1(703)993-4383/+1(703)673-8894 Author of “Trees of the Brain, Roots of the Mind<http://www.amazon.com/Trees-Brain-Roots-Giorgio-Ascoli/dp/0262028980/>” (MIT Press, 2015<http://mitpress.mit.edu/books/trees-brain-roots-mind>) Founding Editor-in-Chief, Neuroinformatics<http://link.springer.com/journal/12021> |
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From: NeuroMorpho A. <nm...@gm...> - 2017-07-21 22:14:47
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Dear colleagues, We’re pleased to announce the July 19, 2017 release of Version 7.2 of NeuroMorpho.Org<http://neuromorpho.org/>, adding 7721 reconstructions from 83 new datasets. The repository now provides access to 70,025 cells and passed 7 million downloads in 163 countries. Please visit the What’s new page<http://neuromorpho.org/WIN.jsp> for details on the added data and other updates. The literature coverage was also updated to include publications through June 2017. We are continuously grateful to all the data contributors<http://neuromorpho.org/acknowl.jsp#DC> who freely share their hard-won tracings with the community. We appreciate any and all feedback and comments. Our apologies if you receive multiple versions of this message through cross-listing. Sincerely, The NeuroMorpho.Org team<http://neuromorpho.org/acknowl.jsp#NMO> ---------------- Giorgio Ascoli<http://krasnow1.gmu.edu/cn3/ascoli>, PhD University Professor Bioengineering Department<http://bioengineering.gmu.edu/>, Volgenau School of Engineering<http://volgenau.gmu.edu/> Neuroscience Program<http://neuroscience.gmu.edu/>, Krasnow Institute for Advanced Study<http://krasnow1.gmu.edu/> Director, Center for Neural Informatics, Structures, & Plasticity<http://krasnow1.gmu.edu/cn3> MS2A1 - George Mason University<http://gmu.edu/>, Fairfax, VA 22030-4444 Ph. +1(703)993-4383/+1(703)673-8894 Author of “Trees of the Brain, Roots of the Mind<http://www.amazon.com/Trees-Brain-Roots-Giorgio-Ascoli/dp/0262028980/>” (MIT Press, 2015<http://mitpress.mit.edu/books/trees-brain-roots-mind>) Founding Editor-in-Chief, Neuroinformatics<http://link.springer.com/journal/12021> |
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From: Jaeger, D. <dj...@em...> - 2017-06-06 20:30:03
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Dear Susan, Genesis can certainly be run as a batch job. We have been doing this for many years. First, use nxgenesis to get rid of the graphics. Second, if you want to use different parameters for each job while using the same .g command file, use environment variables to transmit the parameters. I am attaching a script that does reads environment variables (actually 2 versions of this), and also puts the parameter values in the file names so that one can tell what is what afterwards (the Genesis binary data format carries no metainformation unfortunately). For a systematic parameter manipulation package, see https://github.com/cengique/param-search-neuro maintained by Cengiz Gunay. He first started this software as a postdoc in my lab and it has since been used on a variety of cluster configurations. It is also becoming available as Genesis simulation toolkit on the NSG (https://www.nsgportal.org/). We have just started to use the NSG instead of a local cluster. -Dieter -----Original Message----- From: Susan Chacko [mailto:su...@he...] Sent: Monday, June 05, 2017 4:19 PM To: gen...@li... Subject: [Genesis-sim-users] question about Genesis via batch systems Hi all, I've installed Genesis on a cluster here at the NIH (see https://hpc.nih.gov/apps/genesis.html). I can see how to run it in an interactive session, as I've documented on our webpage. Can Genesis be run as a detached batch job? I looked through the Genesis documentation, but I couldn't see how to make that work. We run the Slurm batch system here, and I'd like to add instructions for running batch jobs, to guide our users in the right direction. Any info or suggestions much appreciated, Susan Chacko. -- Susan Chacko, Ph.D. HPC @ NIH Staff ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Genesis-sim-users mailing list Gen...@li... https://lists.sourceforge.net/lists/listinfo/genesis-sim-users ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). |
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From: Susan C. <su...@he...> - 2017-06-06 19:31:37
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Many thanks for all the responses. I'll give it a try and let you know if I have problems. Susan On 6/6/17 2:20 PM, Dave Beeman wrote: > Also, see the Doc genesis.txt and Simulations.txt for suggestions on running in the background. > > Dave > > On 06/06/2017 10:15 AM, Hugo Cornelis wrote: >> >> >> Hi Susan, >> >> I use the screen command for running Genesis in the background. >> >> The screen command detaches the terminal session from your window and continues running in the >> background. After detaching, you can reattach a few hours or days later via the same screen command. >> >> Typing screen in a system shell creates a new session. >> >> Typing control-a control-d in such a session detaches that session and puts it in the background. >> Running processes continue running (but they must not use any X-Window calls). >> >> Typing screen -ls in a system shell lists all the active screen sessions. >> >> Typing screen -r in a system shell reattach to a running background session. Output to the >> terminal is preserved and will be displayed. >> >> The screen command also has logging capabilities. >> >> I hope this helps. >> >> Hugo >> >> >> >> On Mon, Jun 5, 2017 at 10:19 PM, Susan Chacko <su...@he... <mailto:su...@he...>> >> wrote: >> >> Hi all, >> >> I've installed Genesis on a cluster here at the NIH (see https://hpc.nih.gov/apps/genesis.html >> <https://hpc.nih.gov/apps/genesis.html>). I can see how to run it in an interactive session, >> as I've documented on our webpage. Can Genesis be run as a detached batch job? I looked >> through the Genesis documentation, but I couldn't see how to make that work. We run the Slurm >> batch system here, and I'd like to add instructions for running batch jobs, to guide our users >> in the right direction. >> >> Any info or suggestions much appreciated, >> Susan Chacko. >> >> -- >> Susan Chacko, Ph.D. >> HPC @ NIH Staff >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> Genesis-sim-users mailing list >> Gen...@li... <mailto:Gen...@li...> >> https://lists.sourceforge.net/lists/listinfo/genesis-sim-users >> <https://lists.sourceforge.net/lists/listinfo/genesis-sim-users> >> >> >> >> >> -- >> Hugo >> >> >> >> -- >> >> Hugo Cornelis, Ph.D. >> >> Agora Classica -- CTO >> http://www.agoraclassica.com/ <http://www.genesis-sim.org/> >> >> GENESIS-3 -- lead architect >> http://www.genesis-sim.org/ >> >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org!http://sdm.link/slashdot >> >> >> _______________________________________________ >> Genesis-sim-users mailing list >> Gen...@li... >> https://lists.sourceforge.net/lists/listinfo/genesis-sim-users > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > > _______________________________________________ > Genesis-sim-users mailing list > Gen...@li... > https://lists.sourceforge.net/lists/listinfo/genesis-sim-users > |
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From: Dave B. <db...@Co...> - 2017-06-06 18:54:48
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Also, see the Doc genesis.txt and Simulations.txt for suggestions on running in the background. Dave On 06/06/2017 10:15 AM, Hugo Cornelis wrote: > > > Hi Susan, > > I use the screen command for running Genesis in the background. > > The screen command detaches the terminal session from your window and > continues running in the background. After detaching, you can > reattach a few hours or days later via the same screen command. > > Typing screen in a system shell creates a new session. > > Typing control-a control-d in such a session detaches that session and > puts it in the background. Running processes continue running (but > they must not use any X-Window calls). > > Typing screen -ls in a system shell lists all the active screen sessions. > > Typing screen -r in a system shell reattach to a running background > session. Output to the terminal is preserved and will be displayed. > > The screen command also has logging capabilities. > > I hope this helps. > > Hugo > > > > On Mon, Jun 5, 2017 at 10:19 PM, Susan Chacko <su...@he... > <mailto:su...@he...>> wrote: > > Hi all, > > I've installed Genesis on a cluster here at the NIH (see > https://hpc.nih.gov/apps/genesis.html > <https://hpc.nih.gov/apps/genesis.html>). I can see how to run it > in an interactive session, as I've documented on our webpage. Can > Genesis be run as a detached batch job? I looked through the > Genesis documentation, but I couldn't see how to make that work. > We run the Slurm batch system here, and I'd like to add > instructions for running batch jobs, to guide our users in the > right direction. > > Any info or suggestions much appreciated, > Susan Chacko. > > -- > Susan Chacko, Ph.D. > HPC @ NIH Staff > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Genesis-sim-users mailing list > Gen...@li... > <mailto:Gen...@li...> > https://lists.sourceforge.net/lists/listinfo/genesis-sim-users > <https://lists.sourceforge.net/lists/listinfo/genesis-sim-users> > > > > > -- > Hugo > > > > -- > > Hugo Cornelis, Ph.D. > > Agora Classica -- CTO > http://www.agoraclassica.com/ <http://www.genesis-sim.org/> > > GENESIS-3 -- lead architect > http://www.genesis-sim.org/ > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > Genesis-sim-users mailing list > Gen...@li... > https://lists.sourceforge.net/lists/listinfo/genesis-sim-users |
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From: Hugo C. <hug...@gm...> - 2017-06-06 16:15:45
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Hi Susan, I use the screen command for running Genesis in the background. The screen command detaches the terminal session from your window and continues running in the background. After detaching, you can reattach a few hours or days later via the same screen command. Typing screen in a system shell creates a new session. Typing control-a control-d in such a session detaches that session and puts it in the background. Running processes continue running (but they must not use any X-Window calls). Typing screen -ls in a system shell lists all the active screen sessions. Typing screen -r in a system shell reattach to a running background session. Output to the terminal is preserved and will be displayed. The screen command also has logging capabilities. I hope this helps. Hugo On Mon, Jun 5, 2017 at 10:19 PM, Susan Chacko <su...@he...> wrote: > Hi all, > > I've installed Genesis on a cluster here at the NIH (see > https://hpc.nih.gov/apps/genesis.html). I can see how to run it in an > interactive session, as I've documented on our webpage. Can Genesis be run > as a detached batch job? I looked through the Genesis documentation, but I > couldn't see how to make that work. We run the Slurm batch system here, and > I'd like to add instructions for running batch jobs, to guide our users in > the right direction. > > Any info or suggestions much appreciated, > Susan Chacko. > > -- > Susan Chacko, Ph.D. > HPC @ NIH Staff > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Genesis-sim-users mailing list > Gen...@li... > https://lists.sourceforge.net/lists/listinfo/genesis-sim-users > -- Hugo -- Hugo Cornelis, Ph.D. Agora Classica -- CTO http://www.agoraclassica.com/ <http://www.genesis-sim.org/> GENESIS-3 -- lead architect http://www.genesis-sim.org/ |
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From: Susan C. <su...@he...> - 2017-06-05 20:37:57
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Hi all, I've installed Genesis on a cluster here at the NIH (see https://hpc.nih.gov/apps/genesis.html). I can see how to run it in an interactive session, as I've documented on our webpage. Can Genesis be run as a detached batch job? I looked through the Genesis documentation, but I couldn't see how to make that work. We run the Slurm batch system here, and I'd like to add instructions for running batch jobs, to guide our users in the right direction. Any info or suggestions much appreciated, Susan Chacko. -- Susan Chacko, Ph.D. HPC @ NIH Staff |
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